Washington – A total of $1.3 billion that the Pentagon shipped to its force commanders in Afghanistan between 2004 and 2014 for the most critical reconstruction projects can’t be accounted for by the Defense Department, 60 percent of all such spending under an emergency program, an internal report released Thursday shows.

About 70 percent of the $100 billion the United States has spent to rebuild Afghanistan during 13 1/2 years of war has gone through the Pentagon, with the rest distributed by the US Agency for International Development and other civilian departments. A small portion of the Pentagon’s money went directly to American military officers there in a bid to bypass bureaucracy and rush the aid to urgently needed roads, bridges, schools, hospitals, water-treatment plants and other essential infrastructure.

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A yearlong investigation by John F. Sopko, the US special inspector general for Afghanistan reconstruction, or SIGAR, found that the Pentagon could not – or would not – provide basic information about what happened to six in 10 dollars of $2.26 billion it spent over the course of a decade on the Commander’s Emergency Response Program, which goes by its acronym CERP in military circles.

“In reviewing this data, SIGAR found that the Department of Defense could only provide financial information relating to the disbursement of funds for CERP projects totaling $890 million (40 percent) of the approximately $2.2 billion in obligated funds at that time,” Sopko’s report said.

When Sopko’s staff divided the Pentagon expenditures into 20 categories set under the emergency program, from transportation and education to healthcare, agriculture, water and sanitation, by far the largest category was in a 21st category that the inspector general termed “Unknown.”

That category applied to 5,163 projects, compared with 4,494 projects in all of the 20 defined areas put together.

The Pentagon did not respond directly to Sopko’s main findings in comment he sought while conducting the probe, and which he released along with his report on the investigation.

In one somewhat cryptic comment, the US Central Command, which oversees military operations in Afghanistan and 19 other countries in the Middle East and Central Asia, suggested that some of the CERP money was redirected from reconstruction aid to more direct war needs.

“Although the (SIGAR) report is technically accurate, it did not discuss the Counter Insurgency strategies in relationship to CERP,” the Central Command stated in a Feb. 25, 2015, email to Sopko’s office. “In addition (to) the 20 uses of CERP funds, it was also used as a tool for Counter Insurgency.”

However, with the bulk of the Afghanistan war’s $800 billion price tag for the United States having gone to battlefield needs, it is not clear why money set aside for urgent reconstruction needs would need to pay for counterinsurgency, which has been a core part of the US military campaign there since the October 2001 invasion following the Sept. 11 terror attacks.

Brief descriptions of the 20 categories defined by Pentagon regulation under the emergency-response program, also included in Sopko’s report, do not mention counterinsurgency.

The closest categories to anything battle-related are “condolence payments” to Afghan civilians, or their families, who die or are injured because of the war and “hero payments” to the surviving spouses or next of kin of Afghan soldiers or police killed in the conflict.

The SIGAR report suggests how intertwined US military and reconstruction efforts in Afghanistan became, and how difficult it is to separate the two.

While Sopko found that the CERP money was disbursed for projects throughout virtually all of Afghanistan’s 35 provinces, almost half of it went to the two – Kandahar and Helmand – that have seen the most Taliban activity and the war’s bloodiest battles.

A total of 1,507 American service members have perished in Kandahar and Helmand provinces, almost two-thirds of all 2,357 US fatalities in the war.

Kandahar, dominated by ethnic Pashtuns on the Pakistan border in southern Afghanistan, has been a Taliban hub since the insurgents took it over in 1994 during the civil war that followed Soviet occupation of the Central Asia country.

About $289 million, almost one-third of the CERP money that the Pentagon could account for, was spent in Kandahar, according to the new SIGAR report.

The Pentagon may have good reason to redirect money away from reconstruction projects: SIGAR, which Congress established in 2008 to track US nonmilitary aid to Afghanistan, has issued dozens of reports documenting billions of dollars lost to waste or corruption.

Sopko, however, has broadened his focus to examine what happened to some US funds for Afghan soldiers and police.

In a report released last July, Sopko and his staff found that the Pentagon had shipped Afghan security forces tens of thousands of excessive AK-47 assault rifles and other weapons since 2004, and that many had gone missing, raising concerns that they’d fallen into the hands of Taliban or other insurgent rebels.

An earlier report, released in October 2013, concluded that the United States was continuing to give Afghan security forces a planned $1.4 billion to buy gasoline through 2018 despite evidence that some of the money had been siphoned off for other, unexplained, uses.

Annual spending on the Commander’s Emergency Response Program peaked in 2009 at $500 million, or 23 percent of its total disbursements over the decade. It was in that year that then newly elected President Barack Obama surged additional troops to Afghanistan, fulfilling a 2008 campaign promise.

The end of 2009 was also when CERP’s operating procedures were brought into alignment with a broader US program called Afghanistan First, which “encourages the use of Afghan contractors to the greatest extent possible,” according to the new SIGAR report.

The number of US troops in Afghanistan reached its highest level at 100,000 in August 2010. Only 9,800 remain, although Obama has slowed his withdrawal plan, promising the Afghan government to keep that number there through this year and delaying the final exit to 2017.

Clarification:This article was inadvertently posted before an embargo on the SIGAR report lifted at 12:01 a.m. Friday.

Correction: An earlier version of this article erroneously described the distribution of US aid among the Pentagon and nonmilitary government agencies. About 70 percent of such aid goes through the Pentagon.

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